3W32

EGFR kinase domain complexed with compound 20a


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.200 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Design and synthesis of novel pyrimido[4,5-b]azepine derivatives as HER2/EGFR dual inhibitors

Kawakita, Y.Seto, M.Ohashi, T.Tamura, T.Yusa, T.Miki, H.Iwata, H.Kamiguchi, H.Tanaka, T.Sogabe, S.Ohta, Y.Ishikawa, T.

(2013) Bioorg.Med.Chem. 21: 2250-2261

  • DOI: 10.1016/j.bmc.2013.02.014
  • Primary Citation of Related Structures:  3W33

  • PubMed Abstract: 
  • A novel 7,6 fused bicyclic scaffold, pyrimido[4,5-b]azepine was designed to fit into the ATP binding site of the HER2/EGFR proteins. The synthesis of this scaffold was accomplished by an intramolecular Claisen-type condensation. As the results of opt ...

    A novel 7,6 fused bicyclic scaffold, pyrimido[4,5-b]azepine was designed to fit into the ATP binding site of the HER2/EGFR proteins. The synthesis of this scaffold was accomplished by an intramolecular Claisen-type condensation. As the results of optimization lead us to 4-anilino and 6-functional groups, we discovered 6-substituted amide derivative 19b, which has a 1-benzothiophen-4-yloxy group attached to the 4-anilino group. An X-ray co-crystal structure of 19b with EGFR demonstrated that the N-1 and N-3 nitrogens of the pyrimido[4,5-b]azepine scaffold make hydrogen-bonding interactions with the main chain NH of Met793 and the side chain of Thr854 via a water-mediated hydrogen bond network, respectively. In addition, the NH proton at the 9-position makes an additional hydrogen bond with the carbonyl group of Met793, as we expected. Compound 19b revealed potent HER2/EGFR kinase (IC50: 24/36 nM) and BT474 cell growth (GI50: 18 nM) inhibitory activities based on its pseudo-irreversible (PI) profile.


    Organizational Affiliation

    Pharmaceutical Research Division, Takeda Pharmaceutical Co., Ltd, 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan. Electronic address: youichi.kawakita@takeda.com.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Epidermal growth factor receptor
A
330Homo sapiensGene Names: EGFR (ERBB, ERBB1, HER1)
EC: 2.7.10.1
Find proteins for P00533 (Homo sapiens)
Go to Gene View: EGFR
Go to UniProtKB:  P00533
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
W32
Query on W32

Download SDF File 
Download CCD File 
A
4-({3-chloro-4-[3-(trifluoromethyl)phenoxy]phenyl}amino)-N-[2-(methylsulfonyl)ethyl]-8,9-dihydro-7H-pyrimido[4,5-b]azepine-6-carboxamide
C25 H23 Cl F3 N5 O4 S
QRXMEGUJRZKMEO-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
W32IC50: 75 nM (100) BINDINGDB
W32IC50: 75 nM BINDINGMOAD
W32IC50: 75 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.200 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 46.443α = 90.00
b = 68.306β = 90.00
c = 103.273γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
ADSCdata collection
HKL-2000data reduction
MOLREPphasing
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-03-06
    Type: Initial release
  • Version 1.1: 2013-08-14
    Type: Database references